Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013541.1 Corchorus olitorius cultivar O-4 contig13574, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 11808
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Found at i:354 original size:76 final size:76
Alignment explanation
Indices: 214--362 Score: 192
Period size: 76 Copynumber: 2.0 Consensus size: 76
204 CACTCACCTT
* * * *
214 GAAATCATCGCTTTGACCAAAACTGATTTTGAAACATCTTTTGATTAAAACACCGTCATTCCTTT
1 GAAATCATAGCTTTGACCAAAACTGATTTTGAAAAATCTTTTGATTAAAACACCATCATCCCTTT
*
279 GCTTACAGCTC
66 GCTCACAGCTC
* * * * *
290 GAAATCATAGTTTTGACTAAAACTGATTTTGAAAAATCTTTTTGTTTGAAAC-TCATCATCCCTT
1 GAAATCATAGCTTTGACCAAAACTGATTTTGAAAAATC-TTTTGATTAAAACACCATCATCCCTT
354 TGCTCACAG
65 TGCTCACAG
363 TCCAGATAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
76 51 0.82
77 11 0.18
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (76 bp):
GAAATCATAGCTTTGACCAAAACTGATTTTGAAAAATCTTTTGATTAAAACACCATCATCCCTTT
GCTCACAGCTC
Found at i:8595 original size:21 final size:20
Alignment explanation
Indices: 8567--8614 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
8557 ATCATGTAAA
*
8567 ATGC-AAATGTGAGATAAAT
1 ATGCAAAATGTGAGACAAAT
*
8586 ATGCGAAAATGTGATACAAAT
1 ATGC-AAAATGTGAGACAAAT
8607 ATGCAAAA
1 ATGCAAAA
8615 GAACACAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.16
20 4 0.16
21 17 0.68
ACGTcount: A:0.50, C:0.08, G:0.19, T:0.23
Consensus pattern (20 bp):
ATGCAAAATGTGAGACAAAT
Found at i:8753 original size:27 final size:28
Alignment explanation
Indices: 8723--8788 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 28
8713 AAATTACCAC
8723 AATGCCCCCT-GAAGCACAAATGACTAA
1 AATGCCCCCTGGAAGCACAAATGACTAA
* **
8750 AATG-CCCCTGGATGTGCAAATGACTAA
1 AATGCCCCCTGGAAGCACAAATGACTAA
8777 AATG-CCCCTGGA
1 AATGCCCCCTGGA
8789 TTTTGAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
26 5 0.14
27 30 0.86
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (28 bp):
AATGCCCCCTGGAAGCACAAATGACTAA
Found at i:8789 original size:27 final size:28
Alignment explanation
Indices: 8739--8813 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 28
8729 CCCTGAAGCA
8739 CAAATGACTAAAATGCCCCTGGA-TGTG
1 CAAATGACTAAAATGCCCCTGGATTGTG
*
8766 CAAATGACTAAAATGCCCCTGGATTTTG
1 CAAATGACTAAAATGCCCCTGGATTGTG
* *
8794 AAAATGACCCAAAATGCCCC
1 CAAATGA-CTAAAATGCCCC
8814 ATAGATGACC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
27 23 0.53
28 9 0.21
29 11 0.26
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.21
Consensus pattern (28 bp):
CAAATGACTAAAATGCCCCTGGATTGTG
Found at i:11324 original size:6 final size:6
Alignment explanation
Indices: 11313--11338 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
11303 CAATTCGAAC
11313 ATGTAT ATGTAT ATGTAT ATGTAT AT
1 ATGTAT ATGTAT ATGTAT ATGTAT AT
11339 ACTATCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (6 bp):
ATGTAT
Found at i:11576 original size:21 final size:21
Alignment explanation
Indices: 11531--11599 Score: 86
Period size: 21 Copynumber: 3.2 Consensus size: 21
11521 TCAAAAAATT
*
11531 ATAGGAAGATTAACAAAATCTC
1 ATAGGGAGATT-ACAAAATCTC
*
11553 ATAGGGAGGTTATCAAAA-CTC
1 ATAGGGAGATTA-CAAAATCTC
*
11574 ATAGGGAGATTACAAAATTTC
1 ATAGGGAGATTACAAAATCTC
11595 ATAGG
1 ATAGG
11600 AGGGTTTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 5 0.12
21 22 0.54
22 14 0.34
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25
Consensus pattern (21 bp):
ATAGGGAGATTACAAAATCTC
Found at i:11666 original size:28 final size:28
Alignment explanation
Indices: 11634--11690 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
11624 AGATTATCAA
11634 AGTTTCATATGAAGTTTATCACAATTTC
1 AGTTTCATATGAAGTTTATCACAATTTC
*
11662 AGTTTCATATGCAGTTTATCACAATTTC
1 AGTTTCATATGAAGTTTATCACAATTTC
11690 A
1 A
11691 TAGGTAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (28 bp):
AGTTTCATATGAAGTTTATCACAATTTC
Found at i:11785 original size:3 final size:3
Alignment explanation
Indices: 11777--11808 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
11767 ACTAGTATAT
11777 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Done.